Semi-quantitative immunohistochemical detection of 5-hydroxymethyl-cytosine reveals conservation of its tissue distribution between amphibians and mammals

5-Hydroxymethyl-cytosine (5-hmC) is a form of modified cytosine, which has recently attracted a considerable attention due to its potential role in transcriptional regulation. According to several reports 5-hydroxymethyl-cytosine distribution is tissue-specific in mammals. Thus, 5-hmC is enriched in embryonic cell populations and in adult neuronal tissue. Here, we describe a novel method of semi-quantitative immunohistochemical detection of 5-hmC and utilize it to assess the levels of this modification in amphibian tissues. We show that, similar to mammalian embryos, 5-hmC is enriched in axolotl tadpoles compared with adult tissues. Our data demonstrate that 5-hmC distribution is tissue-specific in amphibians, and that strong 5-hmC enrichment in neuronal cells is conserved between amphibians and mammals. In addition, we identify 5-hmC-enriched cell populations that are distributed in amphibian skin and connective tissue in a mosaic manner. Our results illustrate that immunochemistry can be successfully used not only for spatial identification of cells enriched with 5-hmC, but also for the semi-quantitative assessment of the levels of this epigenetic modification in single cells of different tissues. © 2012 Landes Bioscience

The starburst phenomenon from the optical/near-IR perspective

The optical/near-IR stellar continuum carries unique information about the stellar population in a galaxy, its mass function and star-formation history. Star-forming regions display rich emission-line spectra from which we can derive the dust and gas distribution, map velocity fields, metallicities and young massive stars and locate shocks and stellar winds. All this information is very useful in the dissection of the starburst phenomenon. We discuss a few of the advantages and limitations of observations in the optical/near-IR region and focus on some results. Special attention is given to the role of interactions and mergers and observations of the relatively dust-free starburst dwarfs. In the future we expect new and refined diagnostic tools to provide us with more detailed information about the IMF, strength and duration of the burst and its triggering mechanisms.Comment: 6 pages, 3 figures, to appear in "Starbursts: from 30 Doradus to Lyman Break Galaxies" 2005, eds. R. de Grijs and R. M. Gonzalez Delgado (Kluwer

The stellar host in blue compact dwarf galaxies: the need for a two-dimensional fit

The structural properties of the low surface brightness stellar host in blue compact dwarf galaxies are often studied by fitting r^{1/n} models to the outer regions of their radial profiles. The limitations imposed by the presence of a large starburst emission overlapping the underlying component makes this kind of analysis a difficult task. We propose a two-dimensional fitting methodology in order to improve the extraction of the structural parameters of the LSB host. We discuss its advantages and weaknesses by using a set of simulated galaxies and compare the results for a sample of eight objects with those already obtained using a one-dimensional technique. We fit a PSF convolved Sersic model to synthetic galaxies, and to real galaxy images in the B, V, R filters. We restrict the fit to the stellar host by masking out the starburst region and take special care to minimize the sky-subtraction uncertainties. In order to test the robustness and flexibility of the method, we carry out a set of fits with synthetic galaxies. Furthermore consistency checks are performed to assess the reliability and accuracy of the derived structural parameters. The more accurate isolation of the starburst emission is the most important advantage and strength of the method. Thus, we fit the host galaxy in a range of surface brightness and in a portion of area larger than in previous published 1D fits with the same dataset. We obtain robust fits for all the sample galaxies, all of which, except one, show Sersic indices n very close to 1, with good agreement in the three bands. These findings suggest that the stellar hosts in BCDs have near-exponential profiles, a result that will help us to understand the mechanisms that form and shape BCD galaxies, and how they relate to the other dwarf galaxy classes.Comment: 22 pages, 15 figures (low resolution), accepted for publication in A&A. A higher resolution version of the figures can be provided upon reques

MinION Analysis and Reference Consortium: Phase 1 data release and analysis

The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologies™ in April 2014, giving public access to their USB-attached miniature sequencing device. The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community. Envisaged as a multi-phased project, this study provides the global community with the Phase 1 data from MARC, where the reproducibility of the performance of the MinION was evaluated at multiple sites. Five laboratories on two continents generated data using a control strain of Escherichia coli K-12, preparing and sequencing samples according to a revised ONT protocol. Here, we provide the details of the protocol used, along with a preliminary analysis of the characteristics of typical runs including the consistency, rate, volume and quality of data produced. Further analysis of the Phase 1 data presented here, and additional experiments in Phase 2 of E. coli from MARC are already underway to identify ways to improve and enhance MinION performance

Imaging Jupiter's radiation belts down to 127 MHz with LOFAR

Context. Observing Jupiter's synchrotron emission from the Earth remains today the sole method to scrutinize the distribution and dynamical behavior of the ultra energetic electrons magnetically trapped around the planet (because in-situ particle data are limited in the inner magnetosphere). Aims. We perform the first resolved and low-frequency imaging of the synchrotron emission with LOFAR at 127 MHz. The radiation comes from low energy electrons (~1-30 MeV) which map a broad region of Jupiter's inner magnetosphere. Methods (see article for complete abstract) Results. The first resolved images of Jupiter's radiation belts at 127-172 MHz are obtained along with total integrated flux densities. They are compared with previous observations at higher frequencies and show a larger extent of the synchrotron emission source (>=4 $R_J$). The asymmetry and the dynamic of east-west emission peaks are measured and the presence of a hot spot at lambda_III=230 {\deg} $\pm$ 25 {\deg}. Spectral flux density measurements are on the low side of previous (unresolved) ones, suggesting a low-frequency turnover and/or time variations of the emission spectrum. Conclusions. LOFAR is a powerful and flexible planetary imager. The observations at 127 MHz depict an extended emission up to ~4-5 planetary radii. The similarities with high frequency results reinforce the conclusion that: i) the magnetic field morphology primarily shapes the brightness distribution of the emission and ii) the radiating electrons are likely radially and latitudinally distributed inside about 2 $R_J$. Nonetheless, the larger extent of the brightness combined with the overall lower flux density, yields new information on Jupiter's electron distribution, that may shed light on the origin and mode of transport of these particles.Comment: 10 pages, 12 figures, accepted for publication in A&A (27/11/2015) - abstract edited because of limited character

Optimized Trigger for Ultra-High-Energy Cosmic-Ray and Neutrino Observations with the Low Frequency Radio Array

When an ultra-high energy neutrino or cosmic ray strikes the Lunar surface a radio-frequency pulse is emitted. We plan to use the LOFAR radio telescope to detect these pulses. In this work we propose an efficient trigger implementation for LOFAR optimized for the observation of short radio pulses.Comment: Submitted to Nuclear Instruments and Methods in Physics Research Section

Star Formation in the Central 400 pc of the Milky Way: Evidence for a Population of Massive YSOs

The central kpc of the Milky Way might be expected to differ significantly from the rest of the Galaxy with regard to gas dynamics and the formation of YSOs. We probe this possibility with mid-infrared observations obtained with IRAC and MIPS on Spitzer and with MSX. We use color-color diagrams and SED fits to explore the nature of YSO candidates (including objects with 4.5 micron excesses possibly due to molecular emission). There is an asymmetry in the distribution of the candidate YSOs, which tend to be found at negative Galactic longitudes; this behavior contrasts with that of the molecular gas, approximately 2/3 of which is at positive longitudes. The small scale height of these objects suggests that they are within the Galactic center region and are dynamically young. They lie between two layers of infrared dark clouds and may have originated from these clouds. We identify new sites for this recent star formation. The methanol masers appear to be associated with young, embedded YSOs characterized by 4.5 micron excesses. We use the SEDs of these sources to estimate their physical characteristics. Within the central 400x50 pc (|l|<1.3\degr and |b|<10') the star formation rate based on the identification of Stage I evolutionary phase of YSO candidates is about 0.14 solar mass/yr. We suggest that a recent burst of star formation took place within the last 10^5 years. This suggestion is also consistent with estimates of star formation rates within the last ~10^7 years showing a peak around 10^5 years ago. Lastly, we find that the Schmidt-Kennicutt Law applies well in the central 400 pc of the Galaxy. This implies that star formation does not appear to be dramatically affected by the extreme physical conditions in the Galactic center region.Comment: 96 pages, ten tables, 35 figures, ApJ (in press), replaced by a revised versio

Detectors for the James Webb Space Telescope Near-Infrared Spectrograph I: Readout Mode, Noise Model, and Calibration Considerations

We describe how the James Webb Space Telescope (JWST) Near-Infrared Spectrograph's (NIRSpec's) detectors will be read out, and present a model of how noise scales with the number of multiple non-destructive reads sampling-up-the-ramp. We believe that this noise model, which is validated using real and simulated test data, is applicable to most astronomical near-infrared instruments. We describe some non-ideal behaviors that have been observed in engineering grade NIRSpec detectors, and demonstrate that they are unlikely to affect NIRSpec sensitivity, operations, or calibration. These include a HAWAII-2RG reset anomaly and random telegraph noise (RTN). Using real test data, we show that the reset anomaly is: (1) very nearly noiseless and (2) can be easily calibrated out. Likewise, we show that large-amplitude RTN affects only a small and fixed population of pixels. It can therefore be tracked using standard pixel operability maps.Comment: 55 pages, 10 figure

The distribution of water in the high-mass star-forming region NGC 6334I

We present observations of twelve rotational transitions of H2O-16, H2O-18, and H2O-17 toward the massive star-forming region NGC 6334 I, carried out with Herschel/HIFI as part of the guaranteed time key program Chemical HErschel Surveys of Star forming regions (CHESS). We analyze these observations to obtain insights into physical processes in this region. We identify three main gas components (hot core, cold foreground, and outflow) in NGC 6334 I and derive the physical conditions in these components. The hot core, identified by the emission in highly excited lines, shows a high excitation temperature of 200 K, whereas water in the foreground component is predominantly in the ortho- and para- ground states. The abundance of water varies between 4 10^-5 (outflow) and 10^-8 (cold foreground gas). This variation is most likely due to the freeze-out of water molecules onto dust grains. The H2O-18/H2O-17 abundance ratio is 3.2, which is consistent with the O-18/O-17 ratio determined from CO isotopologues. The ortho/para ratio in water appears to be relatively low 1.6(1) in the cold, quiescent gas, but close to the equilibrium value of three in the warmer outflow material (2.5(0.8)).Comment: 7 pages, 3 figures, accepted by A&

Apertif 1.4 GHz continuum observations of the Bo\"otes field and their combined view with LOFAR

We present a new image of a 26.5 square degree region in the Bo\"otes constellation obtained at 1.4 GHz using the Aperture Tile in Focus (Apertif) system on the Westerbork Synthesis Radio Telescope. We use a newly developed processing pipeline which includes direction-dependent self-calibration which provides a significant improvement of the quality of the images compared to those released as part of the Apertif first data release. For the Bo\"otes region, we mosaic 187 Apertif images and extract a source catalog. The mosaic image has an angular resolution of 27${\times}$11.5 arcseconds and a median background noise of 40 ${\mu}$Jy/beam. The catalog has 8994 sources and is complete down to the 0.3 mJy level. We combine the Apertif image with LOFAR images of the Bo\"otes field at 54 and 150 MHz to study spectral properties of the sources. We find a spectral flattening towards low flux density sources. Using the spectral index limits from Apertif non-detections we derive that up to 9 percent of the sources have ultra-steep spectra with a slope steeper than -1.2. Steepening of the spectral index with increasing redshift is also seen in the data showing a different dependency for the low-frequency spectral index and the high frequency one. This can be explained by a population of sources having concave radio spectra with a turnover frequency around the LOFAR band. Additionally, we discuss cases of individual extended sources with an interesting resolved spectral structure. With the improved pipeline, we aim to continue processing data from the Apertif wide-area surveys and release the improved 1.4 GHz images of several famous fields.Comment: 13 pages, 9 figures; to be published in A&